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Fioravanti A, Mathelie-Guinlet M, Dufrêne YF, Remaut H. The Bacillus anthracis S-layer is an exoskeleton-like structure that imparts mechanical and osmotic stabilization to the cell wall. PNAS NEXUS 2022; 1:pgac121. [PMID: 36714836 PMCID: PMC9802277 DOI: 10.1093/pnasnexus/pgac121] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 08/02/2022] [Indexed: 02/05/2023]
Abstract
Surface layers (S-layers) are 2D paracrystalline protein monolayers covering the cell envelope of many prokaryotes and archaea. Proposed functions include a role in cell support, as scaffolding structure, as molecular sieve, or as virulence factor. Bacillus anthracis holds two S-layers, composed of Sap or EA1, which interchange in early and late exponential growth phase. We previously found that acute disruption of B. anthracis Sap S-layer integrity, by means of nanobodies, results in severe morphological cell surface defects and cell collapse. Remarkably, this loss of function is due to the destruction of the Sap lattice structure rather than detachment of monomers from the cell surface. Here, we combine force nanoscopy and light microscopy observations to probe the contribution of the S-layer to the mechanical, structural, and functional properties of the cell envelope, which have been so far elusive. Our experiments reveal that cells with a compromised S-layer lattice show a decreased compressive stiffness and elastic modulus. Furthermore, we find that S-layer integrity is required to resist cell turgor under hypotonic conditions. These results present compelling experimental evidence indicating that the S-layers can serve as prokaryotic exoskeletons that support the cell wall in conferring rigidity and mechanical stability to bacterial cells.
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Affiliation(s)
- Antonella Fioravanti
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Marion Mathelie-Guinlet
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
| | - Yves F Dufrêne
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
| | - Han Remaut
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
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2
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Pan J, Kmieciak T, Liu YT, Wildenradt M, Chen YS, Zhao Y. Quantifying molecular- to cellular-level forces in living cells. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2021; 54:483001. [PMID: 34866655 PMCID: PMC8635116 DOI: 10.1088/1361-6463/ac2170] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Mechanical cues have been suggested to play an important role in cell functions and cell fate determination, however, such physical quantities are challenging to directly measure in living cells with single molecule sensitivity and resolution. In this review, we focus on two main technologies that are promising in probing forces at the single molecule level. We review their theoretical fundamentals, recent technical advancements, and future directions, tailored specifically for interrogating mechanosensitive molecules in live cells.
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Affiliation(s)
- Jason Pan
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America
| | - Tommy Kmieciak
- Department of Engineering Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America
| | - Yen-Ting Liu
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America
| | - Matthew Wildenradt
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America
| | - Yun-Sheng Chen
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America
| | - Yang Zhao
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, 208 N. Wright Street, Urbana, IL 61801, United States of America
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3
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Schuster B, Sleytr UB. S-Layer Ultrafiltration Membranes. MEMBRANES 2021; 11:275. [PMID: 33918014 PMCID: PMC8068369 DOI: 10.3390/membranes11040275] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/30/2021] [Accepted: 04/03/2021] [Indexed: 11/29/2022]
Abstract
Monomolecular arrays of protein subunits forming surface layers (S-layers) are the most common outermost cell envelope components of prokaryotic organisms (bacteria and archaea). Since S-layers are periodic structures, they exhibit identical physicochemical properties for each constituent molecular unit down to the sub-nanometer level. Pores passing through S-layers show identical size and morphology and are in the range of ultrafiltration membranes. The functional groups on the surface and in the pores of the S-layer protein lattice are accessible for chemical modifications and for binding functional molecules in very precise fashion. S-layer ultrafiltration membranes (SUMs) can be produced by depositing S-layer fragments as a coherent (multi)layer on microfiltration membranes. After inter- and intramolecular crosslinking of the composite structure, the chemical and thermal resistance of these membranes was shown to be comparable to polyamide membranes. Chemical modification and/or specific binding of differently sized molecules allow the tuning of the surface properties and molecular sieving characteristics of SUMs. SUMs can be utilized as matrices for the controlled immobilization of functional biomolecules (e.g., ligands, enzymes, antibodies, and antigens) as required for many applications (e.g., biosensors, diagnostics, enzyme- and affinity-membranes). Finally, SUM represent unique supporting structures for stabilizing functional lipid membranes at meso- and macroscopic scale.
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Affiliation(s)
- Bernhard Schuster
- Institute for Synthetic Bioarchitectures, Department of NanoBiotechnology, BOKU—University of Natural Resources and Life Sciences, Vienna, Muthgasse 11, 1190 Vienna, Austria
| | - Uwe B. Sleytr
- Institute for Synthetic Bioarchitectures, Department of NanoBiotechnology, BOKU—University of Natural Resources and Life Sciences, Vienna, Muthgasse 11, 1190 Vienna, Austria
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Li J, Webster TJ, Tian B. Functionalized Nanomaterial Assembling and Biosynthesis Using the Extremophile Deinococcus radiodurans for Multifunctional Applications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1900600. [PMID: 30925017 DOI: 10.1002/smll.201900600] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/05/2019] [Indexed: 06/09/2023]
Abstract
The development of functionalized nanomaterial biosynthesis processes is important to expand many cutting-edge nanomaterial application areas. However, unclear synthesis mechanisms and low synthesis efficiency under various chemical stresses have limited the use of these biomaterials. Deinococcus radiodurans is an extreme bacterium well known for its exceptional resistance to radiation oxidants and electrophilic agents. This extremophile, which possesses a spontaneous self-assembled surface-layer (S-layer), has been an optimal model organism to study microbial nanomaterial biotemplates and biosynthesis under various stresses. This review summarizes the S-layers from D. radiodurans as an excellent biotemplate for various pre-synthesized nanomaterials and multiple applications, and highlights recent progresses about the biosynthesis of functionalized gold nanoparticles (AuNPs), silver nanoparticles (AgNPs), as well as gold and silver bimetallic nanoparticles using D. radiodurans. Their formation mechanisms, properties, and applications are discussed and summarized to provide significant insights into the design or modification of functionalized nanomaterials via natural materials. Grand challenges and future directions to realize the multifunctional applications of these nanomaterials are highlighted for a better understanding of their biosynthesis mechanisms and functionalized modifications.
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Affiliation(s)
- Jiulong Li
- Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
- Department of Chemical Engineering, Northeastern University, 313 Snell Engineering Center, Boston, MA, 02115, USA
| | - Thomas J Webster
- Department of Chemical Engineering, Northeastern University, 313 Snell Engineering Center, Boston, MA, 02115, USA
| | - Bing Tian
- Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
- Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan, School of Chemistry and Chemical Engineering, Shihezi University, Shihezi, 832003, China
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Ganser C, Uchihashi T. Microtubule self-healing and defect creation investigated by in-line force measurements during high-speed atomic force microscopy imaging. NANOSCALE 2018; 11:125-135. [PMID: 30525150 DOI: 10.1039/c8nr07392a] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Microtubules are biopolymers composed of tubulin and play diverse roles in a wide variety of biological processes such as cell division, migration and intracellular transport in eukaryotic cells. To perform their functions, microtubules are mechanically stressed and, thereby, susceptible to structural defects. Local variations in mechanical properties caused by these defects modulate their biological functions, including binding and transportation of microtubule-associated proteins. Therefore, assessing the local mechanical properties of microtubules and analyzing their dynamic response to mechanical stimuli provide insight into fundamental processes. It is, however, not trivial to control defect formation, gather mechanical information at the same time, and subsequently image the result at a high temporal resolution at the molecular level with minimal delay. In this work, we describe the so-called in-line force curve mode based on high-speed atomic force microscopy. This method is directly applied to create defects in microtubules at the level of tubulin dimers and monitor the following dynamic processes around the defects. Furthermore, force curves obtained during defect formation provide quantitative mechanical information to estimate the bonding energy between tubulin dimers.
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Affiliation(s)
- Christian Ganser
- Department of Physics, Nagoya University, Chikusa-ku, Furo-cho, 464-8602 Nagoya, Aichi, Japan.
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6
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Atomic force microscopy for the investigation of molecular and cellular behavior. Micron 2016; 89:60-76. [DOI: 10.1016/j.micron.2016.07.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 07/27/2016] [Indexed: 12/19/2022]
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7
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Kreplak L. Introduction to Atomic Force Microscopy (AFM) in Biology. ACTA ACUST UNITED AC 2016; 85:17.7.1-17.7.21. [PMID: 27479503 DOI: 10.1002/cpps.14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The atomic force microscope (AFM) has the unique capability of imaging biological samples with molecular resolution in buffer solution over a wide range of time scales from milliseconds to hours. In addition to providing topographical images of surfaces with nanometer- to angstrom-scale resolution, forces between single molecules and mechanical properties of biological samples can be investigated from the nano-scale to the micro-scale. Importantly, the measurements are made in buffer solutions, allowing biological samples to "stay alive" within a physiological-like environment while temporal changes in structure are measured-e.g., before and after addition of chemical reagents. These qualities distinguish AFM from conventional imaging techniques of comparable resolution, e.g., electron microscopy (EM). This unit provides an introduction to AFM on biological systems and describes specific examples of AFM on proteins, cells, and tissues. The physical principles of the technique and methodological aspects of its practical use and applications are also described. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Laurent Kreplak
- Department of Physics & Atmospheric Science, Dalhousie University, Halifax, Canada
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8
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Mechanics of Bacterial Cells and Initial Surface Colonisation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 915:245-60. [DOI: 10.1007/978-3-319-32189-9_15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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9
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Jacquot A, Sakamoto C, Razafitianamarahavo A, Caillet C, Merlin J, Fahs A, Ghigo JM, Duval JFL, Beloin C, Francius G. The dynamics and pH-dependence of Ag43 adhesins' self-association probed by atomic force spectroscopy. NANOSCALE 2014; 6:12665-12681. [PMID: 25208582 DOI: 10.1039/c4nr03312d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Self-associating auto-transporter (SAAT) adhesins are two-domain cell surface proteins involved in bacteria auto-aggregation and biofilm formation. Antigen 43 (Ag43) is a SAAT adhesin commonly found in Escherichia coli whose variant Ag43a has been shown to promote persistence of uropathogenic E. coli within the bladder. The recent resolution of the tri-dimensional structure of the 499 amino-acids' β-domain in Ag43a has shed light on the possible mechanism governing the self-recognition of SAAT adhesins, in particular the importance of trans-interactions between the L shaped β-helical scaffold of two α-domains of neighboring adhesins. In this study, we use single-molecule force spectroscopy (SMFS) and dynamic force spectroscopy (DFS) to unravel the dynamics of Ag43-self association under various pH and molecular elongation rate conditions that mimic the situations encountered by E. coli in its natural environment. Results evidenced an important stretchability of Ag43α with unfolding of sub-domains leading to molecular extension as long as 150 nm. Nanomechanical analysis of molecular stretching data suggested that self-association of Ag43 can lead to the formation of dimers and tetramers driven by rapid and weak cis- as well as slow but strong trans-interaction forces with a magnitude as large as 100-250 pN. The dynamics of cis- and trans-interactions were demonstrated to be strongly influenced by pH and applied shear force, thus suggesting that environmental conditions can modulate Ag43-mediated aggregation of bacteria at the molecular level.
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Affiliation(s)
- Adrien Jacquot
- Université de Lorraine, Laboratoire de Chimie Physique et Microbiologie pour l'Environnement, UMR 7564, Villers-lès-Nancy, F-54601, France
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10
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Sleytr UB, Schuster B, Egelseer E, Pum D. S-layers: principles and applications. FEMS Microbiol Rev 2014; 38:823-64. [PMID: 24483139 PMCID: PMC4232325 DOI: 10.1111/1574-6976.12063] [Citation(s) in RCA: 257] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 01/10/2014] [Accepted: 01/13/2014] [Indexed: 01/12/2023] Open
Abstract
Monomolecular arrays of protein or glycoprotein subunits forming surface layers (S-layers) are one of the most commonly observed prokaryotic cell envelope components. S-layers are generally the most abundantly expressed proteins, have been observed in species of nearly every taxonomical group of walled bacteria, and represent an almost universal feature of archaeal envelopes. The isoporous lattices completely covering the cell surface provide organisms with various selection advantages including functioning as protective coats, molecular sieves and ion traps, as structures involved in surface recognition and cell adhesion, and as antifouling layers. S-layers are also identified to contribute to virulence when present as a structural component of pathogens. In Archaea, most of which possess S-layers as exclusive wall component, they are involved in determining cell shape and cell division. Studies on structure, chemistry, genetics, assembly, function, and evolutionary relationship of S-layers revealed considerable application potential in (nano)biotechnology, biomimetics, biomedicine, and synthetic biology.
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Affiliation(s)
- Uwe B. Sleytr
- Institute of BiophysicsDepartment of NanobiotechnologyUniversity of Natural Resources and Life SciencesViennaAustria
| | - Bernhard Schuster
- Institute of Synthetic BiologyDepartment of NanobiotechnologyUniversity of Natural Resources and Life SciencesViennaAustria
| | - Eva‐Maria Egelseer
- Institute of BiophysicsDepartment of NanobiotechnologyUniversity of Natural Resources and Life SciencesViennaAustria
| | - Dietmar Pum
- Institute of BiophysicsDepartment of NanobiotechnologyUniversity of Natural Resources and Life SciencesViennaAustria
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11
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Ando T, Uchihashi T, Scheuring S. Filming biomolecular processes by high-speed atomic force microscopy. Chem Rev 2014; 114:3120-88. [PMID: 24476364 PMCID: PMC4076042 DOI: 10.1021/cr4003837] [Citation(s) in RCA: 250] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Indexed: 12/21/2022]
Affiliation(s)
- Toshio Ando
- Department of Physics, and Bio-AFM Frontier
Research Center, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
- CREST,
Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi 332-0012, Japan
| | - Takayuki Uchihashi
- Department of Physics, and Bio-AFM Frontier
Research Center, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
- CREST,
Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi 332-0012, Japan
| | - Simon Scheuring
- U1006
INSERM/Aix-Marseille Université, Parc Scientifique et Technologique
de Luminy Bâtiment Inserm TPR2 bloc 5, 163 avenue de Luminy, 13288 Marseille Cedex 9, France
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12
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Günther TJ, Suhr M, Raff J, Pollmann K. Immobilization of microorganisms for AFM studies in liquids. RSC Adv 2014. [DOI: 10.1039/c4ra03874f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Reproducible immobilization method even for living eukaryotes and prokaryotes on polyelectrolyte coated surfaces for high resolution AFM imaging in liquids.
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Affiliation(s)
- Tobias J. Günther
- Helmholtz-Zentrum Dresden-Rossendorf
- Institute for Resource Ecology and Helmholtz Institute Freiberg for Resource Technology
- 01328 Dresden, Germany
| | - Matthias Suhr
- Helmholtz-Zentrum Dresden-Rossendorf
- Institute of Resource Ecology
- 01328 Dresden, Germany
| | - Johannes Raff
- Helmholtz-Zentrum Dresden-Rossendorf
- Institute for Resource Ecology and Helmholtz Institute Freiberg for Resource Technology
- 01328 Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf
- Institute of Resource Ecology
| | - Katrin Pollmann
- Helmholtz-Zentrum Dresden-Rossendorf
- Institute for Resource Ecology and Helmholtz Institute Freiberg for Resource Technology
- 01328 Dresden, Germany
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13
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Nanomechanical probing of the septum and surrounding substances on Streptococcus mutans cells and biofilms. Colloids Surf B Biointerfaces 2013; 110:356-62. [DOI: 10.1016/j.colsurfb.2013.05.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Revised: 05/07/2013] [Accepted: 05/09/2013] [Indexed: 12/21/2022]
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Bujalowski PJ, Oberhauser AF. Tracking unfolding and refolding reactions of single proteins using atomic force microscopy methods. Methods 2013; 60:151-60. [PMID: 23523554 DOI: 10.1016/j.ymeth.2013.03.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 03/07/2013] [Accepted: 03/11/2013] [Indexed: 11/26/2022] Open
Abstract
During the last two decades single-molecule manipulation techniques such as atomic force microscopy (AFM) has risen to prominence through their unique capacity to provide fundamental information on the structure and function of biomolecules. Here we describe the use of single-molecule AFM to track protein unfolding and refolding pathways, enzymatic catalysis and the effects of osmolytes and chaperones on protein stability and folding. We will outline the principles of operation for two different AFM pulling techniques: length clamp and force-clamp and discuss prominent applications. We provide protocols for the construction of polyproteins which are amenable for AFM experiments, the preparation of different coverslips, choice and calibration of AFM cantilevers. We also discuss the selection criteria for AFM recordings, the calibration of AFM cantilevers, protein sample preparations and analysis of the obtained data.
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Affiliation(s)
- Paul J Bujalowski
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, TX 77555, USA
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15
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Abstract
The alarming rise in drug-resistant hospital ‘superbugs’ and the associated increase in fatalities is driving the development of technologies to search for new antibiotics and improve disease diagnostics. One of the most successful drug targets is the bacterial cell wall, an evolutionary feature of virtually all prokaryotes and vital for their survival by providing mechanical strength. The recent discovery of bacterial cytoskeletal proteins analogous to the key force-bearing machinery in eukaryotes also provides new opportunities for drug discovery, but little is known about their mechanical role in bacteria. In the present short article, I review recent developments in the field of nanotechnology to investigate the mechanical mechanisms of action of potent antibiotics on cell wall and cytoskeletal targets with unprecedented spatial, temporal and force resolution and the development of a new generation of nanomechanical devices to detect pathogens for point-of-care diagnostics.
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Abstract
High-speed atomic force microscopy (HS-AFM) is now materialized. It allows direct visualization of dynamic structural changes and dynamic processes of functioning biological molecules in physiological solutions, at high spatiotemporal resolution. Dynamic molecular events unselectively appear in detail in an AFM movie, facilitating our understanding of how biological molecules operate to function. This review describes a historical overview of technical development towards HS-AFM, summarizes elementary devices and techniques used in the current HS-AFM, and then highlights recent imaging studies. Finally, future challenges of HS-AFM studies are briefly discussed.
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Affiliation(s)
- Toshio Ando
- Department of Physics and Bio-AFM Frontier Research Center, Kanazawa University, Kakuma-machi, Kanazawa, Japan
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17
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Affiliation(s)
- Francisco Zaera
- Department of Chemistry, University of California, Riverside, California 92521, United States
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18
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Casillas-Ituarte NN, Lower BH, Lamlertthon S, Fowler VG, Lower SK. Dissociation rate constants of human fibronectin binding to fibronectin-binding proteins on living Staphylococcus aureus isolated from clinical patients. J Biol Chem 2012; 287:6693-701. [PMID: 22219202 DOI: 10.1074/jbc.m111.285692] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Staphylococcus aureus is part of the indigenous microbiota of humans. Sometimes, S. aureus bacteria enter the bloodstream, where they form infections on implanted cardiovascular devices. A critical, first step in such infections is a bond that forms between fibronectin-binding protein (FnBP) on S. aureus and host proteins, such as fibronectin (Fn), that coat the surface of implants in vivo. In this study, native FnBPs on living S. aureus were shown to form a mechanically strong conformational structure with Fn by atomic force microscopy. The tensile acuity of this bond was probed for 46 bloodstream isolates, each from a patient with a cardiovascular implant. By analyzing the force spectra with the worm-like chain model, we determined that the binding events were consistent with a multivalent, cluster bond consisting of ~10 or ~80 proteins in parallel. The dissociation rate constant (k(off), s(-1)) of each multibond complex was determined by measuring strength as a function of the loading rate, normalized by the number of bonds. The bond lifetime (1/k(off)) was two times longer for bloodstream isolates from patients with an infected device (1.79 or 69.47 s for the 10- or 80-bond clusters, respectively; n = 26 isolates) relative to those from patients with an uninfected device (0.96 or 34.02 s; n = 20 isolates). This distinction could not be explained by different amounts of FnBP, as confirmed by Western blots. Rather, amino acid polymorphisms within the Fn-binding repeats of FnBPA explain, at least partially, the statistically (p < 0.05) longer bond lifetime for isolates associated with an infected cardiovascular device.
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Abstract
Intrinsically disordered regions (IDRs) of proteins are very thin and hence hard to be visualized by electron microscopy. Thus far, only high-speed atomic force microscopy (HS-AFM) can visualize them. The molecular movies identify the alignment of IDRs and ordered regions in an intrinsically disordered protein (IDP) and show undulation motion of the IDRs. The visualized tail-like structures contain the information of mechanical properties of the IDRs. Here, we describe methods of HS-AFM visualization of IDPs and methods of analyzing the obtained images to characterize IDRs.
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Affiliation(s)
- Toshio Ando
- Department of Physics and Bio-AFM Frontier Research Center, Kanazawa University, Kanazawa, Japan.
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20
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Müller SA, Engel A. Looking back at a quarter-century of research at the Maurice E. Müller Institute for Structural Biology. J Struct Biol 2011; 177:3-13. [PMID: 22115996 DOI: 10.1016/j.jsb.2011.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Revised: 11/04/2011] [Accepted: 11/05/2011] [Indexed: 10/15/2022]
Abstract
The Maurice E. Müller Institute, embedded in the infrastructure of the Biozentrum, University of Basel, was founded in 1985 and financed by the Maurice E. Müller Foundation of Switzerland. For 26 years its two founders, Ueli Aebi and Andreas Engel, pursued the vision of integrated structural biology. This paper reviews selected publications issuing from the Maurice E. Müller Institute for Structural Biology and marks the end of this era.
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Affiliation(s)
- Shirley A Müller
- Center for Cellular Imaging and Nano Analytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
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21
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Horejs C, Ristl R, Tscheliessnig R, Sleytr UB, Pum D. Single-molecule force spectroscopy reveals the individual mechanical unfolding pathways of a surface layer protein. J Biol Chem 2011; 286:27416-24. [PMID: 21690085 PMCID: PMC3149335 DOI: 10.1074/jbc.m111.251322] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 06/15/2011] [Indexed: 12/14/2022] Open
Abstract
Surface layers (S-layers) represent an almost universal feature of archaeal cell envelopes and are probably the most abundant bacterial cell proteins. S-layers are monomolecular crystalline structures of single protein or glycoprotein monomers that completely cover the cell surface during all stages of the cell growth cycle, thereby performing their intrinsic function under a constant intra- and intermolecular mechanical stress. In gram-positive bacteria, the individual S-layer proteins are anchored by a specific binding mechanism to polysaccharides (secondary cell wall polymers) that are linked to the underlying peptidoglycan layer. In this work, atomic force microscopy-based single-molecule force spectroscopy and a polyprotein approach are used to study the individual mechanical unfolding pathways of an S-layer protein. We uncover complex unfolding pathways involving the consecutive unfolding of structural intermediates, where a mechanical stability of 87 pN is revealed. Different initial extensibilities allow the hypothesis that S-layer proteins adapt highly stable, mechanically resilient conformations that are not extensible under the presence of a pulling force. Interestingly, a change of the unfolding pathway is observed when individual S-layer proteins interact with secondary cell wall polymers, which is a direct signature of a conformational change induced by the ligand. Moreover, the mechanical stability increases up to 110 pN. This work demonstrates that single-molecule force spectroscopy offers a powerful tool to detect subtle changes in the structure of an individual protein upon binding of a ligand and constitutes the first conformational study of surface layer proteins at the single-molecule level.
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Affiliation(s)
| | - Robin Ristl
- From the Department for Nanobiotechnology and
| | - Rupert Tscheliessnig
- the Austrian Centre of Industrial Biotechnology, c/o Institute for Biotechnology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | | | - Dietmar Pum
- From the Department for Nanobiotechnology and
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22
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Lower SK. Atomic force microscopy to study intermolecular forces and bonds associated with bacteria. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011; 715:285-99. [PMID: 21557071 DOI: 10.1007/978-94-007-0940-9_18] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Atomic force microscopy (AFM) operates on a very different principle than other forms of microscopy, such as optical microscopy or electron microscopy. The key component of an AFM is a cantilever that bends in response to forces that it experiences as it touches another surface. Forces as small as a few picoNewtons can be detected and probed with AFM. AFM has become very useful in biological sciences because it can be used on living cells that are immersed in water. AFM is particularly useful when the cantilever is modified with chemical groups (e.g. amine or carboxylic groups), small beads (e.g. glass or latex), or even a bacterium. This chapter describes how AFM can be used to measure forces and bonds between a bacterium and another surface. This paper also provides an example of the use of AFM on Staphylococcus aureus, a Gram-positive bacterium that is often associated with biofilms in humans.
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23
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Acosta JC, Hwang G, Polesel-Maris J, Régnier S. A tuning fork based wide range mechanical characterization tool with nanorobotic manipulators inside a scanning electron microscope. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2011; 82:035116. [PMID: 21456797 DOI: 10.1063/1.3541776] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
This study proposes a tuning fork probe based nanomanipulation robotic system for mechanical characterization of ultraflexible nanostructures under scanning electron microscope. The force gradient is measured via the frequency modulation of a quartz tuning fork and two nanomanipulators are used for manipulation of the nanostructures. Two techniques are proposed for attaching the nanostructure to the tip of the tuning fork probe. The first technique involves gluing the nanostructure for full range characterization whereas the second technique uses van der Waals and electrostatic forces in order to avoid destroying the nanostructure. Helical nanobelts (HNB) are proposed for the demonstration of the setup. The nonlinear stiffness behavior of HNBs during their full range tensile studies is clearly revealed for the first time. Using the first technique, this was between 0.009 N/m for rest position and 0.297 N/m before breaking of the HNB with a resolution of 0.0031 N/m. For the second experiment, this was between 0.014 N/m for rest position and 0.378 N/m before detaching of the HNB with a resolution of 0.0006 N/m. This shows the wide range sensing of the system for potential applications in mechanical property characterization of ultraflexible nanostructures.
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Affiliation(s)
- Juan Camilo Acosta
- Institut des Systèmes Intelligents et de Robotique Université Pierre et Marie Curie, CNRS UMR 7222 4 Place Jussieu, 75252 Paris Cedex, France.
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24
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Müller SA, Müller DJ, Engel A. Assessing the structure and function of single biomolecules with scanning transmission electron and atomic force microscopes. Micron 2011; 42:186-95. [DOI: 10.1016/j.micron.2010.10.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 10/05/2010] [Accepted: 10/05/2010] [Indexed: 11/30/2022]
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25
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Lower SK, Yongsunthon R, Casillas-Ituarte NN, Taylor ES, DiBartola AC, Lower BH, Beveridge TJ, Buck AW, Fowler VG. A tactile response in Staphylococcus aureus. Biophys J 2011; 99:2803-11. [PMID: 21044577 DOI: 10.1016/j.bpj.2010.08.063] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2010] [Revised: 07/16/2010] [Accepted: 08/30/2010] [Indexed: 01/22/2023] Open
Abstract
It is well established that bacteria are able to respond to temporal gradients (e.g., by chemotaxis). However, it is widely held that prokaryotes are too small to sense spatial gradients. This contradicts the common observation that the vast majority of bacteria live on the surface of a solid substrate (e.g., as a biofilm). Herein we report direct experimental evidence that the nonmotile bacterium Staphylococcus aureus possesses a tactile response, or primitive sense of touch, that allows it to respond to spatial gradients. Attached cells recognize their substrate interface and localize adhesins toward that region. Braille-like avidity maps reflect a cell's biochemical sensory response and reveal ultrastructural regions defined by the actual binding activity of specific proteins.
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26
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Allison DP, Mortensen NP, Sullivan CJ, Doktycz MJ. Atomic force microscopy of biological samples. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2011; 2:618-34. [PMID: 20672388 DOI: 10.1002/wnan.104] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The ability to evaluate structural-functional relationships in real time has allowed scanning probe microscopy (SPM) to assume a prominent role in post genomic biological research. In this mini-review, we highlight the development of imaging and ancillary techniques that have allowed SPM to permeate many key areas of contemporary research. We begin by examining the invention of the scanning tunneling microscope (STM) by Binnig and Rohrer in 1982 and discuss how it served to team biologists with physicists to integrate high-resolution microscopy into biological science. We point to the problems of imaging nonconductive biological samples with the STM and relate how this led to the evolution of the atomic force microscope (AFM) developed by Binnig, Quate, and Gerber, in 1986. Commercialization in the late 1980s established SPM as a powerful research tool in the biological research community. Contact mode AFM imaging was soon complemented by the development of non-contact imaging modes. These non-contact modes eventually became the primary focus for further new applications including the development of fast scanning methods. The extreme sensitivity of the AFM cantilever was recognized and has been developed into applications for measuring forces required for indenting biological surfaces and breaking bonds between biomolecules. Further functional augmentation to the cantilever tip allowed development of new and emerging techniques including scanning ion-conductance microscopy (SICM), scanning electrochemical microscope (SECM), Kelvin force microscopy (KFM) and scanning near field ultrasonic holography (SNFUH).
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Affiliation(s)
- David P Allison
- Biosciences Division, Oak Ridge National Laboratory, TN 37831-6445, USA
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27
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The Structure of Bacterial S-Layer Proteins. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 103:73-130. [DOI: 10.1016/b978-0-12-415906-8.00004-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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28
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Suzuki Y, Yokokawa M, Yoshimura SH, Takeyasu K. Biological Application of Fast-Scanning Atomic Force Microscopy. SCANNING PROBE MICROSCOPY IN NANOSCIENCE AND NANOTECHNOLOGY 2 2011. [DOI: 10.1007/978-3-642-10497-8_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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29
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Lacayo CI, Malkin AJ, Holman HYN, Chen L, Ding SY, Hwang MS, Thelen MP. Imaging cell wall architecture in single Zinnia elegans tracheary elements. PLANT PHYSIOLOGY 2010; 154:121-33. [PMID: 20592039 PMCID: PMC2938135 DOI: 10.1104/pp.110.155242] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Accepted: 06/23/2010] [Indexed: 05/18/2023]
Abstract
The chemical and structural organization of the plant cell wall was examined in Zinnia elegans tracheary elements (TEs), which specialize by developing prominent secondary wall thickenings underlying the primary wall during xylogenesis in vitro. Three imaging platforms were used in conjunction with chemical extraction of wall components to investigate the composition and structure of single Zinnia TEs. Using fluorescence microscopy with a green fluorescent protein-tagged Clostridium thermocellum family 3 carbohydrate-binding module specific for crystalline cellulose, we found that cellulose accessibility and binding in TEs increased significantly following an acidified chlorite treatment. Examination of chemical composition by synchrotron radiation-based Fourier-transform infrared spectromicroscopy indicated a loss of lignin and a modest loss of other polysaccharides in treated TEs. Atomic force microscopy was used to extensively characterize the topography of cell wall surfaces in TEs, revealing an outer granular matrix covering the underlying meshwork of cellulose fibrils. The internal organization of TEs was determined using secondary wall fragments generated by sonication. Atomic force microscopy revealed that the resulting rings, spirals, and reticulate structures were composed of fibrils arranged in parallel. Based on these combined results, we generated an architectural model of Zinnia TEs composed of three layers: an outermost granular layer, a middle primary wall composed of a meshwork of cellulose fibrils, and inner secondary wall thickenings containing parallel cellulose fibrils. In addition to insights in plant biology, studies using Zinnia TEs could prove especially productive in assessing cell wall responses to enzymatic and microbial degradation, thus aiding current efforts in lignocellulosic biofuel production.
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Heinisch JJ, Dufrêne YF. Is there anyone out there?--Single-molecule atomic force microscopy meets yeast genetics to study sensor functions. Integr Biol (Camb) 2010; 2:408-15. [PMID: 20648385 DOI: 10.1039/c0ib00012d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The ability to react to environmental stress is a key feature of microbial cells, which frequently involves the fortification of their cell wall as a primary step. In the model yeast Saccharomyces cerevisiae the biosynthesis of the cell wall is regulated by the so-called cell wall integrity signal transduction pathway, which starts with the detection of cell surface stress by a small family of five membrane-spanning sensors (Wsc1-Wsc3, Mid2, Mtl1). Although genetic evidence indicated that these proteins act as mechanosensors, direct in vivo evidence for their function remained scarce. Here, we review a new approach integrating the tools and concepts of genetics with those of nanotechnology. We show how atomic force microscopy can be combined with advanced protein design by yeast genetics, to study the function and the mechanical properties of yeast sensors in living cells down to the single molecule level. We anticipate that this novel integrated technology will enable a paradigm shift in cell biology, so that pertinent questions can be addressed, such as the nanomechanics of single sensors and receptors, and how they distribute across the cell surface when they respond to extracellular stress.
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Affiliation(s)
- Jürgen J Heinisch
- Universität Osnabrück, Fachbereich Biologie/Chemie, AG Genetik, Osnabrück, Germany.
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31
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Buck AW, Fowler VG, Yongsunthon R, Liu J, DiBartola AC, Que YA, Moreillon P, Lower SK. Bonds between fibronectin and fibronectin-binding proteins on Staphylococcus aureus and Lactococcus lactis. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:10764-10770. [PMID: 20218549 PMCID: PMC2893610 DOI: 10.1021/la100549u] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Revised: 03/02/2010] [Indexed: 05/28/2023]
Abstract
Bacterial cell-wall-associated fibronectin binding proteins A and B (FnBPA and FnBPB) form bonds with host fibronectin. This binding reaction is often the initial step in prosthetic device infections. Atomic force microscopy was used to evaluate binding interactions between a fibronectin-coated probe and laboratory-derived Staphylococcus aureus that are (i) defective in both FnBPA and FnBPB (fnbA fnbB double mutant, DU5883), (ii) capable of expressing only FnBPA (fnbA fnbB double mutant complemented with pFNBA4), or (iii) capable of expressing only FnBPB (fnbA fnbB double mutant complemented with pFNBB4). These experiments were repeated using Lactococcus lactis constructs expressing fnbA and fnbB genes from S. aureus. A distinct force signature was observed for those bacteria that expressed FnBPA or FnBPB. Analysis of this force signature with the biomechanical wormlike chain model suggests that parallel bonds form between fibronectin and FnBPs on a bacterium. The strength and covalence of bonds were evaluated via nonlinear regression of force profiles. Binding events were more frequent (p < 0.01) for S. aureus expressing FnBPA or FnBPB than for the S. aureus double mutant. The binding force, frequency, and profile were similar between the FnBPA and FnBPB expressing strains of S. aureus. The absence of both FnBPs from the surface of S. aureus removed its ability to form a detectable bond with fibronectin. By contrast, ectopic expression of FnBPA or FnBPB on the surface of L. lactis conferred fibronectin binding characteristics similar to those of S. aureus. These measurements demonstrate that fibronectin-binding adhesins FnBPA and FnBPB are necessary and sufficient for the binding of S. aureus to prosthetic devices that are coated with host fibronectin.
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Affiliation(s)
| | - Vance G. Fowler
- Duke University Medical Center, Durham, North Carolina
- Duke Clinical Research Institute, Durham, North Carolina
| | | | - Jie Liu
- The Ohio State University, Columbus, Ohio
| | | | - Yok-Ai Que
- Massachusetts General Hospital, Boston, Massachusetts
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32
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Nanocharacterization in dentistry. Int J Mol Sci 2010; 11:2523-45. [PMID: 20640166 PMCID: PMC2904930 DOI: 10.3390/ijms11062523] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Revised: 06/05/2010] [Accepted: 06/07/2010] [Indexed: 11/26/2022] Open
Abstract
About 80% of US adults have some form of dental disease. There are a variety of new dental products available, ranging from implants to oral hygiene products that rely on nanoscale properties. Here, the application of AFM (Atomic Force Microscopy) and optical interferometry to a range of dentistry issues, including characterization of dental enamel, oral bacteria, biofilms and the role of surface proteins in biochemical and nanomechanical properties of bacterial adhesins, is reviewed. We also include studies of new products blocking dentine tubules to alleviate hypersensitivity; antimicrobial effects of mouthwash and characterizing nanoparticle coated dental implants. An outlook on future “nanodentistry” developments such as saliva exosomes based diagnostics, designing biocompatible, antimicrobial dental implants and personalized dental healthcare is presented.
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33
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Fantner GE, Barbero RJ, Gray DS, Belcher AM. Kinetics of antimicrobial peptide activity measured on individual bacterial cells using high-speed atomic force microscopy. NATURE NANOTECHNOLOGY 2010; 5:280-5. [PMID: 20228787 PMCID: PMC3905601 DOI: 10.1038/nnano.2010.29] [Citation(s) in RCA: 243] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2009] [Accepted: 02/03/2010] [Indexed: 05/15/2023]
Abstract
Observations of real-time changes in living cells have contributed much to the field of cellular biology. The ability to image whole, living cells with nanometre resolution on a timescale that is relevant to dynamic cellular processes has so far been elusive. Here, we investigate the kinetics of individual bacterial cell death using a novel high-speed atomic force microscope optimized for imaging live cells in real time. The increased time resolution (13 s per image) allows the characterization of the initial stages of the action of the antimicrobial peptide CM15 on individual Escherichia coli cells with nanometre resolution. Our results indicate that the killing process is a combination of a time-variable incubation phase (which takes seconds to minutes to complete) and a more rapid execution phase.
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Affiliation(s)
- Georg E Fantner
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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34
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Assessing Biological Samples with Scanning Probes. SINGLE MOLECULE SPECTROSCOPY IN CHEMISTRY, PHYSICS AND BIOLOGY 2010. [DOI: 10.1007/978-3-642-02597-6_21] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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35
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Bizzarri AR, Cannistraro S. The application of atomic force spectroscopy to the study of biological complexes undergoing a biorecognition process. Chem Soc Rev 2010; 39:734-49. [DOI: 10.1039/b811426a] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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36
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Hamit-Eminovski J, Eskilsson K, Arnebrant T. Change in surface properties of Microthrix parvicella upon addition of polyaluminium chloride as characterized by atomic force microscopy. BIOFOULING 2010; 26:323-331. [PMID: 20087804 DOI: 10.1080/08927010903584060] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The filamentous bacterium Microthrix parvicella causes severe separation and foaming problems at wastewater treatment plants (WWTPs). An effective control of the bacterium in activated sludge WWTPs can be accomplished by dosage with polyaluminium chloride (PAX-14). The purpose of this study was to investigate whether addition of PAX-14 affects surface properties such as the hydrophobicity of the bacterium and to study the exopolymers of M. parvicella that host surface-associated enzymes. To this end, force measurements by atomic force microscopy were carried out to measure the interactions between hydrophilic and hydrophobized tips and the bacterium surface. Addition of PAX-14 caused no changes in the hydrophobicity of the bacterium surface but the data indicate that it collapsed the polymeric layer likely due to electrostatic screening. It is concluded that the collapse of the polymeric layer may affect the transport of substrates (eg free fatty acids) to the bacterium and hence the competitiveness of M. parvicella compared to the other bacteria present in activated sludge.
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Affiliation(s)
- Jildiz Hamit-Eminovski
- Faculty of Health and Society, Biomedical Laboratory Science and Technology, Malmo University, Malmo, Sweden.
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37
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Modern Atomic Force Microscopy and Its Application to the Study of Genome Architecture. SCANNING PROBE MICROSCOPY IN NANOSCIENCE AND NANOTECHNOLOGY 2010. [DOI: 10.1007/978-3-642-03535-7_20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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38
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Goldsbury CS, Scheuring S, Kreplak L. Introduction to Atomic Force Microscopy (AFM) in Biology. ACTA ACUST UNITED AC 2009; Chapter 17:17.7.1-17.7.19. [DOI: 10.1002/0471140864.ps1707s58] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
| | | | - Laurent Kreplak
- Dalhousie University, Department of Physics & Atmospheric Science Halifax Canada
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39
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Bizzarri AR, Cannistraro S. Atomic Force Spectroscopy in Biological Complex Formation: Strategies and Perspectives. J Phys Chem B 2009; 113:16449-64. [DOI: 10.1021/jp902421r] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Anna Rita Bizzarri
- Biophysics and Nanoscience Centre, CNISM, Facoltà di Scienze, Università della Tuscia, Largo dell’Università, 01100 Viterbo, Italy
| | - Salvatore Cannistraro
- Biophysics and Nanoscience Centre, CNISM, Facoltà di Scienze, Università della Tuscia, Largo dell’Università, 01100 Viterbo, Italy
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40
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Scheuring S, Sturgis JN. Atomic force microscopy of the bacterial photosynthetic apparatus: plain pictures of an elaborate machinery. PHOTOSYNTHESIS RESEARCH 2009; 102:197-211. [PMID: 19266309 DOI: 10.1007/s11120-009-9413-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Accepted: 02/10/2009] [Indexed: 05/27/2023]
Abstract
Photosynthesis both in the past and present provides the vast majority of the energy used on the planet. The purple photosynthetic bacteria are a group of organisms that are able to perform photosynthesis using a particularly simple system that has been much studied. The main molecular constituents required for photosynthesis in these organisms are a small number of transmembrane pigment-protein complexes. These are able to function together with a high quantum efficiency (about 95%) to convert light energy into chemical potential energy. While the structure of the various proteins have been solved for several years, direct studies of the supramolecular assembly of these complexes in native membranes needed maturity of the atomic force microscope (AFM). Here, we review the novel findings and the direct conclusions that could be drawn from high-resolution AFM analysis of photosynthetic membranes. These conclusions rely on the possibility that the AFM brings of obtaining molecular resolution images of large membrane areas and thereby bridging the resolution gap between atomic structures and cellular ultrastructure.
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Affiliation(s)
- Simon Scheuring
- Institut Curie, UMR168-CNRS, 26 Rue d’Ulm, 75248 Paris, France.
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41
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Tang J, Ebner A, Kraxberger B, Leitner M, Hykollari A, Kepplinger C, Grunwald C, Gruber HJ, Tampé R, Sleytr UB, Ilk N, Hinterdorfer P. Detection of metal binding sites on functional S-layer nanoarrays using single molecule force spectroscopy. J Struct Biol 2009; 168:217-22. [DOI: 10.1016/j.jsb.2009.02.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Revised: 02/02/2009] [Accepted: 02/05/2009] [Indexed: 11/25/2022]
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42
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Gonçalves RP, Buzhysnskyy N, Scheuring S. Mini review on the structure and supramolecular assembly of VDAC. J Bioenerg Biomembr 2009; 40:133-8. [PMID: 18683037 DOI: 10.1007/s10863-008-9141-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The Voltage Dependent Anion Channel (VDAC) is the most abundant protein in the outer membrane of mitochondria. This strategic localization puts it at the heart of a great number of phenomena. Its recent implication in apoptosis is an example of the major importance of this protein and has created a surge of interest in VDAC. There is no atomic-resolution structure allowing a better understanding of the function of VDAC, so alternative techniques to X-ray diffraction have been used to study VDAC. Here we discuss structural models from folding predictions and review data acquired by Atomic Force Microscopy (AFM) imaging that allowed to observe VDAC's structure and supramolecular organization in the mitochondrial outer membrane.
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Affiliation(s)
- Rui Pedro Gonçalves
- Laboratory of Cell Biophysics, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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43
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Dupres V, Alsteens D, Pauwels K, Dufrêne YF. In vivo imaging of S-layer nanoarrays on Corynebacterium glutamicum. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:9653-9655. [PMID: 19642621 DOI: 10.1021/la902238q] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Crystalline bacterial cell surface layers (S-layers) are monomolecular arrays of (glyco)proteins that have recently produced a wealth of new opportunities in nanotechnology. Whereas the in vitro imaging of isolated S-layers is well established, their direct imaging on live cells remains very challenging. Here we use atomic force microscopy (AFM) to visualize S-layer nanoarrays on living Corynebacterium glutamicum bacteria. We demonstrate the presence of two highly ordered surface layers. The most external layer represents the hexagonal S-layer, and the inner layer displays regular patterns of nanogrooves that could act as a biomolecular template promoting the 2-D assembly of S-layer monomers. These nanoscale analyses open new avenues for understanding the structure of protein monomolecular arrays, which is a crucial challenge in current nanoscience and life science research.
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Affiliation(s)
- Vincent Dupres
- Unite de Chimie des Interfaces, Universite Catholique de Louvain, Croix du Sud 2/18, B-1348 Louvain-la-Neuve, Belgium
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44
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Abstract
At the cross-roads of nanoscience and microbiology, the nanoscale analysis of microbial cells using atomic force microscopy (AFM) is an exciting, rapidly evolving research field. Over the past decade, there has been tremendous progress in our use of AFM to observe membrane proteins and live cells at high resolution. Remarkable advances have also been made in applying force spectroscopy to manipulate single membrane proteins, to map surface properties and receptor sites on cells and to measure cellular interactions at the single-cell and single-molecule levels. In addition, recent developments in cantilever nanosensors have opened up new avenues for the label-free detection of microorganisms and bioanalytes.
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Affiliation(s)
- Yves F Dufrêne
- Unité de chimie des interfaces, Université catholique de Louvain, Croix du Sud 2/18, B-1348 Louvain-la-Neuve, Belgium.
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45
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Atomic force microscopy of biological membranes. Biophys J 2009; 96:329-38. [PMID: 19167286 DOI: 10.1016/j.bpj.2008.09.046] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2008] [Accepted: 09/15/2008] [Indexed: 11/21/2022] Open
Abstract
Atomic force microscopy (AFM) is an ideal method to study the surface topography of biological membranes. It allows membranes that are adsorbed to flat solid supports to be raster-scanned in physiological solutions with an atomically sharp tip. Therefore, AFM is capable of observing biological molecular machines at work. In addition, the tip can be tethered to the end of a single membrane protein, and forces acting on the tip upon its retraction indicate barriers that occur during the process of protein unfolding. Here we discuss the fundamental limitations of AFM determined by the properties of cantilevers, present aspects of sample preparation, and review results achieved on reconstituted and native biological membranes.
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46
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Abstract
The atomic force microscope (AFM) is an important tool for studying biological samples due to its ability to image surfaces under liquids. The AFM operates by physical interaction of a cantilever tip with the molecules on the cell surface. Adhesion forces between the tip and cell surface molecules are detected as cantilever deflections. Thus, the cantilever tip can be used to image live cells with atomic resolution and to probe single molecular events in living cells under physiological conditions. Currently, this is the only technique available that directly provides structural, mechanical, and functional information at high resolution. This unit presents the basic AFM components, modes of operation, useful tips for sample preparation, and a short review of AFM applications in microbiology.
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Affiliation(s)
- Andreea Trache
- Department of Systems Biology & Translational Medicine, College of Medicine, Texas A&M Health Science Center, College Station, Texas, USA
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47
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Struckmeier J, Wahl R, Leuschner M, Nunes J, Janovjak H, Geisler U, Hofmann G, Jähnke T, Müller DJ. Fully automated single-molecule force spectroscopy for screening applications. NANOTECHNOLOGY 2008; 19:384020. [PMID: 21832579 DOI: 10.1088/0957-4484/19/38/384020] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
With the introduction of single-molecule force spectroscopy (SMFS) it has become possible to directly access the interactions of various molecular systems. A bottleneck in conventional SMFS is collecting the large amount of data required for statistically meaningful analysis. Currently, atomic force microscopy (AFM)-based SMFS requires the user to tediously 'fish' for single molecules. In addition, most experimental and environmental conditions must be manually adjusted. Here, we developed a fully automated single-molecule force spectroscope. The instrument is able to perform SMFS while monitoring and regulating experimental conditions such as buffer composition and temperature. Cantilever alignment and calibration can also be automatically performed during experiments. This, combined with in-line data analysis, enables the instrument, once set up, to perform complete SMFS experiments autonomously.
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Affiliation(s)
- Jens Struckmeier
- Cellular Machines, Biotechnology Center, Technische Universität Dresden, Tatzberg 47, D-01307 Dresden, Germany. nAmbition GmbH, Tatzberg 47, D-01307 Dresden, Germany
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48
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Miyagi A, Tsunaka Y, Uchihashi T, Mayanagi K, Hirose S, Morikawa K, Ando T. Visualization of Intrinsically Disordered Regions of Proteins by High-Speed Atomic Force Microscopy. Chemphyschem 2008; 9:1859-66. [DOI: 10.1002/cphc.200800210] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Affiliation(s)
- Daniel J. Muller
- Biotechnology Center, Technische Universität Dresden, D-01307 Dresden, Germany
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Janovjak H, Sapra KT, Kedrov A, Müller DJ. From valleys to ridges: exploring the dynamic energy landscape of single membrane proteins. Chemphyschem 2008; 9:954-66. [PMID: 18348129 DOI: 10.1002/cphc.200700662] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Membrane proteins are involved in essential biological processes such as energy conversion, signal transduction, solute transport and secretion. All biological processes, also those involving membrane proteins, are steered by molecular interactions. Molecular interactions guide the folding and stability of membrane proteins, determine their assembly, switch their functional states or mediate signal transduction. The sequential steps of molecular interactions driving these processes can be described by dynamic energy landscapes. The conceptual energy landscape allows to follow the complex reaction pathways of membrane proteins while its modifications describe why and how pathways are changed. Single-molecule force spectroscopy (SMFS) detects, quantifies and locates interactions within and between membrane proteins. SMFS helps to determine how these interactions change with temperature, point mutations, oligomerization and the functional states of membrane proteins. Applied in different modes, SMFS explores the co-existence and population of reaction pathways in the energy landscape of the protein and thus reveals detailed insights into local mechanisms, determining its structural and functional relationships. Here we review how SMFS extracts the defining parameters of an energy landscape such as the barrier position, reaction kinetics and roughness with high precision.
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Affiliation(s)
- Harald Janovjak
- Department. of Molecular & Cell Biology, University of California, Berkeley, 279 Life Sciences Addition, Berkeley, CA 94720-3200, USA
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